GROMACS parameter files (MDPs)
Here are some sample .MDP files for use with GROMACS. Please don't use these blindly; go through them and check that they're reasonable. GROMACS 5+ Gromos 54A7 transmembrane simulation Compiled by Josh. ; MDP file for equilibration of a transmembrane protein in the GROMOS 54A7 force ; field. Generally follows the GROMOS 54a7 paper: ; https://dx.doi.org/10.1007/s00249-011-0700-9 ; INTEGRATION integrator = md dt = 0.002 ; 2 fs step nsteps = 5000000 ; 10 ns simulation nstcomm = 1000 ; remove COM motion every 2 ps (per GROMOS paper) ; OUTPUT CONTROL ; Strangely, this is where GROMACS sets all its output control ; mdrun switches don't change anything nstxout = 0 ; only last ; Steps between writing coords to uncompressed output trajectory nstvout = 0 ; only last ; Steps between writing velocities to uncompressed output trajectory nstfout = 0 ; never ; Steps between writing forces to uncompressed output trajectory nstlog = 5000 ; 100 ps ; Steps between writing energies to log file nstenergy = 5000 ; 100 ps ; Steps between writing energies to energy file nstxout-compressed = 5000 ; 100 ps ; Steps between writing coords to compressed output trajectory compressed-x-precision = 1000 ; Trajectory compression is lossy; this is the precision of that compression ; CUTOFF SCHEME ; Verlet is faster, more parallelisable, more accurate, supports GPUs ; Only use group for the legacy interactions it supports cutoff-scheme = Verlet ; COULOMB INTERACTIONS ; GROMOS 54a7 was parameterised with Reaction field and a triple-range ; cutoff (0.8 nm/1.4 nm), which GROMACS doesn't support; however, PME has been ; shown to be better (https://dx.doi.org/10.1016/j.bpj.2010.04.062) coulombtype = PME rcoulomb = 1.4 ; Reaction field is faster, and can be used instead, especially for smaller, more ; homogenous systems. This speed up is reduced the more CPUs your machine has per ; GPU, unless there are no GPUs. ; Potential shift is v. cheap with Verlet, and doesn't affect forces or sampling ; coulombtype = Reaction-Field ; rcoulomb = 1.4 ; coulomb-modifier = Potential-shift-Verlet ; LJ INTERACTIONS ; Follows the GROMOS 54a7 paper ; Dispersion corrections assume homogeneity beyond the cutoff - not really the ; case for membrane systems. In addition, GROMOS is parameterized for a cutoff ; of 1.4 nm without dispersion corrections. For dispcorr discussion, see ; https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2012-May/071263.html ; See also https://dx.doi.org/10.1021/jp0735987 for inadequacy of existing ; dispersion corrections. ; Potential shift is v. cheap with Verlet, and doesn't affect forces or sampling vdwtype = Cut-off rvdw = 1.4 vdw-modifier = Potential-shift-Verlet dispcorr = no ; TEMPERATURE COUPLING ; Follows the GROMOS 54a7 paper, but substituting berendsen for v-rescale tcoupl = V-rescale tc-grps = Protein non-Protein tau-t = 0.1 0.1 ref-t = 300 300 ; PRESSURE COUPLING ; Follows the GROMOS 54a7 paper ; Berendsen thermostat for equilibration pcoupl = Berendsen ; for equilibration - switch to Parrinello-Rahman for production pcoupltype = semiisotropic tau-p = 0.5 compressibility = 4.5e-5 4.5e-5 ref-p = 1.0 1.0 ; Parrinello-Rahman produces better pressure distribution, ; but is less stable and can oscillate if the box has to dramatically change ; size. Therefore it is best to equilibrate with Berendsen (above) to get the ; box size right, and then switch to PR for production runs. ; pcoupl = Parrinello-Rahman ; pcoupletype = semiisotropic ; tau-p = 5 ; compressibility = 4.5e-5 4.5e-5 ; ref-p = 1.0 1.0 ; If position restraints and pressure coupling are both on, the reference coords ; should be scaled with the box. 'com' and 'all' both work, if one causes crashes ; use the other ;refcoord-scaling = com ; VELOCITY GENERATION gen-vel = yes gen-temp = 300 gen-seed = -1 ; -1 uses a random seed ; CONSTRAINTS ; Constraints on all bonds permit 2 fs time step ; LINCS is faster and more stable ; Use SHAKE if you need angle constraints constraints = all-bonds constraint-algorithm = LINCS continuation = no ;define = -DPOSRES -DPOSRES_FC=1000.0 Category:GROMACS Category:GROMOS